Starting /dee2/code/volunteer_pipeline.sh ERR6133329 current disk space = 1548190380032 free memory = 1599181488 ERR6133329 SRAfilesize 6464ce60a423250968da7457272371eb ERR6133329.sra ERR6133329.sra file validated ERR6133329 is single end ERR6133329 is conventional basespace ERR6133329 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133329_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.96075 37.0 37.0 37.0 33.0 37.0 2 36.52625 37.0 37.0 37.0 37.0 37.0 3 36.60125 37.0 37.0 37.0 37.0 37.0 4 36.40125 37.0 37.0 37.0 37.0 37.0 5 36.5015 37.0 37.0 37.0 37.0 37.0 6 36.568 37.0 37.0 37.0 37.0 37.0 7 38.85525 40.0 37.0 40.0 37.0 40.0 8 38.87725 40.0 37.0 40.0 37.0 40.0 9 38.9065 40.0 37.0 40.0 37.0 40.0 10-11 38.9025 40.0 37.0 40.0 37.0 40.0 12-13 38.848375 40.0 37.0 40.0 37.0 40.0 14-15 38.877250000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.795125 40.0 37.0 40.0 37.0 40.0 18-19 38.724000000000004 40.0 37.0 40.0 37.0 40.0 20-21 38.668375 40.0 37.0 40.0 37.0 40.0 22-23 38.611999999999995 40.0 37.0 40.0 37.0 40.0 24-25 38.466125 40.0 37.0 40.0 37.0 40.0 26-27 38.587125 40.0 37.0 40.0 37.0 40.0 28-29 38.603750000000005 40.0 37.0 40.0 37.0 40.0 30-31 38.553875000000005 40.0 37.0 40.0 37.0 40.0 32-33 38.46025 40.0 37.0 40.0 37.0 40.0 34-35 38.364374999999995 40.0 37.0 40.0 37.0 40.0 36-37 38.268 40.0 37.0 40.0 37.0 40.0 38-39 38.251875 40.0 37.0 40.0 37.0 40.0 40-41 38.088625 40.0 37.0 40.0 37.0 40.0 42-43 37.992125 38.5 37.0 40.0 37.0 40.0 44-45 37.718999999999994 37.0 37.0 40.0 35.0 40.0 46-47 37.620375 37.0 37.0 40.0 37.0 40.0 48-49 37.449625 37.0 37.0 40.0 37.0 40.0 50-51 37.25275 37.0 37.0 40.0 35.0 40.0 52-53 37.129125 37.0 37.0 40.0 33.0 40.0 54-55 37.01375 37.0 37.0 38.5 33.0 40.0 56-57 36.736875 37.0 37.0 37.0 33.0 40.0 58-59 36.442750000000004 37.0 37.0 37.0 33.0 40.0 60-61 36.44525 37.0 37.0 37.0 33.0 40.0 62-63 36.3785 37.0 37.0 37.0 33.0 37.0 64-65 36.197874999999996 37.0 37.0 37.0 33.0 37.0 66-67 35.9795 37.0 37.0 37.0 33.0 37.0 68-69 35.140249999999995 35.0 35.0 37.0 33.0 37.0 70-71 35.45490166248432 37.0 35.0 37.0 33.0 37.0 72-73 35.792455668335144 37.0 37.0 37.0 33.0 37.0 74-75 35.75263288690676 37.0 37.0 37.0 33.0 37.0 76-77 35.81078018064301 37.0 37.0 37.0 33.0 37.0 78-79 35.738517676834604 37.0 37.0 37.0 33.0 37.0 80-81 35.76373317129429 37.0 37.0 37.0 33.0 37.0 82-83 35.55244230572517 37.0 37.0 37.0 33.0 37.0 84-85 35.537387541610805 37.0 35.0 37.0 33.0 37.0 86-87 35.589838581635355 37.0 37.0 37.0 33.0 37.0 88-89 35.60187880391638 37.0 37.0 37.0 33.0 37.0 90-91 35.4542206933051 37.0 33.0 37.0 33.0 37.0 92-93 35.41386610214342 37.0 33.0 37.0 33.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 1.0 22 3.0 23 5.0 24 6.0 25 6.0 26 11.0 27 11.0 28 8.0 29 19.0 30 33.0 31 36.0 32 38.0 33 51.0 34 87.0 35 190.0 36 682.0 37 1277.0 38 1480.0 39 54.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 58.8 10.25 16.875 14.075 2 39.475 30.875000000000004 15.55 14.099999999999998 3 27.1 34.35 18.8 19.75 4 25.575 29.15 19.2 26.075 5 24.2 26.325 29.799999999999997 19.675 6 16.925 41.25 24.825 17.0 7 38.2 25.85 20.575 15.375 8 30.325000000000003 27.0 23.400000000000002 19.275000000000002 9 22.925 28.325 26.05 22.7 10-11 23.075000000000003 30.337500000000002 27.500000000000004 19.0875 12-13 21.3125 29.1625 26.237500000000004 23.2875 14-15 24.099999999999998 31.35 27.437499999999996 17.1125 16-17 26.3125 29.2 23.962500000000002 20.525 18-19 24.0125 26.3 29.7125 19.975 20-21 28.6375 25.05 27.8375 18.475 22-23 32.175 22.175 26.924999999999997 18.725 24-25 24.8625 28.975 27.3875 18.775 26-27 28.8625 24.5375 27.4125 19.1875 28-29 25.137500000000003 26.9125 26.724999999999998 21.224999999999998 30-31 28.175 24.45 28.275 19.1 32-33 25.662499999999998 26.625 27.437499999999996 20.275000000000002 34-35 23.0125 32.3125 24.1625 20.5125 36-37 25.2625 28.275 23.7125 22.75 38-39 28.9536192024003 23.377922240280036 25.453181647705964 22.215276909613703 40-41 23.75 26.575 28.1875 21.4875 42-43 28.249999999999996 30.412499999999998 24.4 16.9375 44-45 21.675 31.337500000000002 28.799999999999997 18.1875 46-47 29.225 24.625 26.237500000000004 19.9125 48-49 25.0375 23.1 29.75 22.112499999999997 50-51 20.9125 27.950000000000003 29.037499999999998 22.1 52-53 28.375 25.7125 24.3 21.6125 54-55 27.875 24.6875 26.9625 20.474999999999998 56-57 27.125 30.675 26.224999999999998 15.975 58-59 22.8 27.400000000000002 31.6875 18.1125 60-61 28.925 29.625 23.2125 18.2375 62-63 21.3125 32.1125 27.462500000000002 19.112499999999997 64-65 21.745654620482682 33.500062523446296 27.885457046392396 16.86882580967863 66-67 22.95 34.5375 24.3125 18.2 68-69 23.175 27.1625 26.937499999999996 22.725 70-71 21.678146524733876 31.133375078271758 27.401377582968067 19.7871008140263 72-73 27.40796772566818 27.50882501260716 29.39989914271306 15.683308119011599 74-75 23.926302414231255 28.716645489199493 29.60609911054638 17.750952986022874 76-77 20.414163364438195 24.453534449699603 26.255912054199154 28.876390131663044 78-79 31.891891891891895 25.945945945945947 25.405405405405407 16.756756756756758 80-81 25.022665457842248 33.85571817122134 24.11604714415231 17.005569226784097 82-83 22.756997122678523 29.24404917603976 28.17159298979859 19.827360711483127 84-85 19.295235581364658 24.152039065593243 34.485944305133955 22.066781047908144 86-87 19.978830378406986 28.605451177560205 25.84016935697274 25.575549087060068 88-89 19.132045514686425 33.48769515744906 27.388197935961895 19.99206139190262 90-91 23.207197671341625 31.6221222545647 26.6075681397195 18.563111934374174 92-93 21.090235512040223 33.64646731939666 26.10478962688542 19.15850754167769 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 1.5 18 2.5 19 1.5 20 1.0 21 4.0 22 6.0 23 6.0 24 6.5 25 5.0 26 5.0 27 9.5 28 13.5 29 17.0 30 25.5 31 36.5 32 46.5 33 58.5 34 70.5 35 75.5 36 107.0 37 157.5 38 190.5 39 198.0 40 233.0 41 238.5 42 233.5 43 263.0 44 226.5 45 178.0 46 161.0 47 162.5 48 138.0 49 137.5 50 228.5 51 246.0 52 160.0 53 129.5 54 193.5 55 151.5 56 55.0 57 53.0 58 39.5 59 19.0 60 15.0 61 15.5 62 12.0 63 10.0 64 6.5 65 8.0 66 8.0 67 6.5 68 7.5 69 6.0 70 3.0 71 0.0 72 1.0 73 1.0 74 0.5 75 1.0 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0125 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0375 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 15.0 71 12.0 72 14.0 73 15.0 74 18.0 75 8.0 76 13.0 77 15.0 78 10.0 79 12.0 80 15.0 81 18.0 82 24.0 83 13.0 84 19.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 3779.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 65.14999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 90.52187260168841 58.975 2 4.911742133537989 6.4 3 1.5349194167306215 3.0 4 0.5372217958557176 1.4000000000000001 5 0.49884881043745205 1.625 6 0.19186492709132769 0.75 7 0.38372985418265537 1.7500000000000002 8 0.23023791250959325 1.2 9 0.07674597083653108 0.44999999999999996 >10 0.9976976208749041 12.3 >50 0.03837298541826554 2.4 >100 0.07674597083653108 9.75 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 204 5.1 No Hit GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 186 4.65 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 96 2.4 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 45 1.125 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 41 1.0250000000000001 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 39 0.975 No Hit TCTCATGGAGAGTTCGATCCTGGCTCAGGATGAACGCTGGCGGCATGCTT 32 0.8 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 31 0.775 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 26 0.65 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 21 0.525 No Hit AACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGA 20 0.5 No Hit CGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAG 19 0.475 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 17 0.42500000000000004 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 16 0.4 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 16 0.4 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 15 0.375 No Hit TCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 15 0.375 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 14 0.35000000000000003 No Hit GATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGC 13 0.325 No Hit GGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTC 12 0.3 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 12 0.3 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 12 0.3 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 12 0.3 No Hit CGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTAT 11 0.27499999999999997 No Hit GAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGC 11 0.27499999999999997 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 11 0.27499999999999997 No Hit CACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGT 11 0.27499999999999997 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 10 0.25 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 10 0.25 No Hit AGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAA 9 0.22499999999999998 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 9 0.22499999999999998 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 8 0.2 No Hit GGGATGATTCTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGG 8 0.2 No Hit GAAGCCTGTGTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGG 8 0.2 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 8 0.2 No Hit GAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTG 8 0.2 No Hit AAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCC 8 0.2 No Hit TAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTA 7 0.17500000000000002 No Hit GGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 7 0.17500000000000002 No Hit GGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAA 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 7 0.17500000000000002 No Hit AATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTAT 7 0.17500000000000002 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 7 0.17500000000000002 No Hit GTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATGGA 7 0.17500000000000002 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 7 0.17500000000000002 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 7 0.17500000000000002 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 6 0.15 No Hit GAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTG 6 0.15 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 6 0.15 No Hit CAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAA 6 0.15 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 6 0.15 No Hit GGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCG 5 0.125 No Hit GGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCATAGAT 5 0.125 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 5 0.125 No Hit TCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCAT 5 0.125 No Hit GTACAAGCTCGTAACGAAGGGCGCGATCTTGCTCGTGAAGGTAATGAAAT 5 0.125 No Hit GGCCCGGACCCTGTCGCCCCACGAGGCGCCGTCAACGAGTCGGGTTGTTT 5 0.125 No Hit GCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATA 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit AGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTG 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAGAGC 20 2.5231071E-5 86.0 2 GCAATAC 20 2.5231071E-5 86.0 7 GGGAGAG 20 2.5231071E-5 86.0 1 CAATACA 20 2.5231071E-5 86.0 8 GAGCAAT 20 2.5231071E-5 86.0 5 AGAGCAA 20 2.5231071E-5 86.0 4 GAGAGCA 20 2.5231071E-5 86.0 3 AATACAA 20 2.5231071E-5 86.0 9 AGCAATA 20 2.5231071E-5 86.0 6 GGCACCC 35 5.1203733E-6 61.42857 7 CTAGGCA 35 5.1203733E-6 61.42857 4 CACCCAG 35 5.1203733E-6 61.42857 9 AGGCACC 35 5.1203733E-6 61.42857 6 GCACCCA 35 5.1203733E-6 61.42857 8 ACCTAGG 35 5.1203733E-6 61.42857 2 CCTAGGC 35 5.1203733E-6 61.42857 3 TAGGCAC 35 5.1203733E-6 61.42857 5 TACCTAG 40 1.1304503E-5 53.75 1 CATCACT 20 6.4128236E-4 45.263157 82-83 ATCACTA 20 6.4128236E-4 45.263157 84-85 >>END_MODULE Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41515 READS because READLEN < 1 Read 41515 spots for ERR6133329.sra Written 41515 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Rejected 41499 READS because READLEN < 1 Rejected 41499 READS because READLEN < 1 Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra Read 41499 spots for ERR6133329.sra Written 41499 spots for ERR6133329.sra SRR ids: ['ERR6133329.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4doql691 ERR6133329.sra spots: 829996 blocks: [[1, 41499], [41500, 82998], [82999, 124497], [124498, 165996], [165997, 207495], [207496, 248994], [248995, 290493], [290494, 331992], [331993, 373491], [373492, 414990], [414991, 456489], [456490, 497988], [497989, 539487], [539488, 580986], [580987, 622485], [622486, 663984], [663985, 705483], [705484, 746982], [746983, 788481], [788482, 829996]] ERR6133329 file size 181515 ERR6133329 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o ERR6133329 ERR6133329_1.fastq Input file: ERR6133329_1.fastq trimmed: ERR6133329-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 00:47:46 2024 >> started Sat Dec 7 00:47:47 2024 >> done (0.759s) 829996 reads processed; of these: 49 ( 0.01%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 829947 (99.99%) reads available; of these: 5238 ( 0.63%) trimmed reads available after processing 824709 (99.37%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 5 0.00% 20 6 0.00% 21 4 0.00% 22 1 0.00% 23 1 0.00% 24 1 0.00% 25 1 0.00% 26 3 0.00% 27 4 0.00% 28 13 0.00% 29 210 0.03% 30 4 0.00% 31 4 0.00% 32 3 0.00% 33 8 0.00% 34 1 0.00% 35 14 0.00% 36 0 0.00% 37 3 0.00% 38 4 0.00% 39 4 0.00% 40 8 0.00% 41 3 0.00% 42 3 0.00% 43 3 0.00% 44 3 0.00% 45 4 0.00% 46 2 0.00% 47 3 0.00% 48 3 0.00% 49 2 0.00% 50 7 0.00% 51 11 0.00% 52 6 0.00% 53 3 0.00% 54 3 0.00% 55 1 0.00% 56 2 0.00% 57 2 0.00% 58 6 0.00% 59 4 0.00% 60 3 0.00% 61 6 0.00% 62 3 0.00% 63 1 0.00% 64 1 0.00% 65 4 0.00% 66 4 0.00% 67 7 0.00% 68 3 0.00% 69 24 0.00% 70 2978 0.36% 71 2918 0.35% 72 2967 0.36% 73 2858 0.34% 74 2835 0.34% 75 2800 0.34% 76 2778 0.33% 77 3048 0.37% 78 3013 0.36% 79 3250 0.39% 80 3202 0.39% 81 3765 0.45% 82 3903 0.47% 83 3454 0.42% 84 3983 0.48% 85 39 0.00% 86 41 0.00% 87 74 0.01% 88 117 0.01% 89 190 0.02% 90 332 0.04% 91 787 0.09% 92 2752 0.33% 93 777432 93.67% 829947 reads passed initial QC criterion=sequence-density sequence-density=1.47 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=17 prefix-density=1.49 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.12 sequence-density-rank=14 fanout-score=76.44 fanout-score-rank=1 prefix-density=8.92 prefix-fanout=1.0 sequence=GGAGATTCCCATATAG Started job on | Dec 07 00:48:01 Started mapping on | Dec 07 00:48:01 Finished on | Dec 07 00:48:06 Mapping speed, Million of reads per hour | 597.56 Number of input reads | 829947 Average input read length | 92 UNIQUE READS: Uniquely mapped reads number | 354550 Uniquely mapped reads % | 42.72% Average mapped length | 90.78 Number of splices: Total | 12142 Number of splices: Annotated (sjdb) | 9306 Number of splices: GT/AG | 11038 Number of splices: GC/AG | 254 Number of splices: AT/AC | 8 Number of splices: Non-canonical | 842 Mismatch rate per base, % | 0.50% Deletion rate per base | 0.05% Deletion average length | 1.82 Insertion rate per base | 0.03% Insertion average length | 1.74 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 431606 % of reads mapped to multiple loci | 52.00% Number of reads mapped to too many loci | 17653 % of reads mapped to too many loci | 2.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.03% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 43791 43791 43791 N_multimapping 431606 431606 431606 N_noFeature 27113 31821 338056 N_ambiguous 13571 1804 54 UnstrandedReadsAssigned:313866 PositiveStrandReadsAssigned:320925 NegativeStrandReadsAssigned:16440 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133329 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR6133329-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 829,947 reads, 539,940 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 825 rounds 52973 ERR6133329.ke.tsv 35125 ERR6133329.se.tsv 88098 total ==> ERR6133329.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 8 14.4133 PNS24243 293 194 0 0 KQK14069 1603 1504 12 19.7224 KQK14071 474 375 0 0 ==> ERR6133329.se.tsv <== BRADI_1g14170v3 12 BRADI_1g53295v3 6 BRADI_1g59795v3 1 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 5 BRADI_1g74790v3 3 BRADI_1g09890v3 0 BRADI_1g77505v3 7 BRADI_1g48960v3 0 ERR6133329 completed mapping pipeline successfully